It looks like you would want an even airflow through the whole PSU. The main heat-generating components are using the sides of the housing as a heat sink. I'm guessing the fan is mostly so the air inside the housing doesn't get too warm, not to cool individual components.
Where is the original air exhaust? If it's near the bottom of the picture, that would confirm my theory. In that case, I would keep the fan placement as close to original as possible (i.e. the blue square).
That's probably not a bad idea, although I doubt it will make much of a difference. But since you're redesigning the whole thing, might as well do it.